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parent41 edited this page Dec 8, 2022 · 5 revisions

All code used to generate the results seen in the manuscript ____

Dependencies

  • minc-toolkit/1.9.17
  • R/3.5.1
  • RMINC/1.5.2.3
  • Matlab/2020a

Steps to run code

  1. Make sure all dependencies are loaded
  2. Clone GitHub repository
git clone https://github.com/parent41/cortical_markers_paper
  1. Download subject-wise vertex data for cortical MRI markers from the Canadian Open Neuroscience Platform (CONP). Put all files in a directory named "vertex_files_20mm_anon" located in the main directory
  2. Run R scripts to generate marker maps (for spatial distribution average, AIC of age effect shape, linear age effect, quadratic age effect)
# First set working directory to the specific analysis folder (e.g., spatial_distribution_average)
cd spatial_distribution_average
# Then run R script
Rscript spatial_distribution_average.R
cd ..

cd AIC_age_effect
Rscript AIC_age_effect.R
cd ..

cd lin_age_effect
Rscript lin_age_effect.R
cd ..

cd quad_age_effect
Rscript quad_age_effect.R
cd ..

cd R1_spatial_distribution_average
Rscript R1_spatial_distribution_average.R
cd ..
  1. Run spin tests in Matlab (scripts to run begin with run_). Set working directory to ./spin_test/scripts/
matlab run_spatial_distribution_average.m
matlab run_R1_spatial_distribution_average.m
matlab run_lin_age_effect.m
matlab run_BigBrain.m
matlab run_AHBA.m
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